In addition to what Dan said, did you source the intel environment scripts
(ifortvars.sh, iccvars.sh, they should be in the same directory as ifort and
icc)? They set up LD_LIBRARY_PATH and PATH for you. However, I can verify
that the intel compilers version 11.1.069 works for installing Amber on my
machine, so if you can roll back, I would suggest trying that to see if it
works.
Good luck!
Jason
On Wed, Dec 1, 2010 at 8:49 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Do you have any previous versions of the intel compiler, and if so
> does compilation complete with them?
>
> Also, could you paste the last 20 or so lines leading up to the error?
> A brief web search suggests this may be related to the '-lsvml' flag
> during the link step (however the post refers to version 11.1 so no
> guarantees, http://software.intel.com/en-us/forums/showthread.php?t=77211
> ).
> Intel is notorious for messing with the linking step (see their MKL
> stuff for more linking headaches) so I'm not surprised something may
> have broken in the new version of the compilers.
>
> Anyway, you could try manually editing your config.h file to remove
> the '-lsvml' flag from the FLIBSF variable and see if compilation is
> able to proceed.
>
> -Dan
>
> On Wed, Dec 1, 2010 at 6:34 AM, Vlad Cojocaru
> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> > Dear Amber community,
> >
> > I am compiling AMBER 11 with the Intel compiler 12.0.0 (which I just
> > purchased)
> > The linking during the *SERIAL* compilation of Amber Tools 1.4 (patched
> > with all bugfixes as of today) fails with error (see below, no other
> > error in make.log):
> >
> > Has anybody experienced this with this version of the Intel compiler?
> > I would appreciate any ideas on how to get rid of this problem
> >
> > Best
> > Vlad
> >
> >
> > Details:
> > -------
> > Architecture
> > Linux name 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010
> > x86_64 x86_64 x86_64 GNU/Linux
> > CPU:
> > 2xAMD 6-core opterons per node
> > OS:
> > CentOS 5.5 (RHL 5.5)
> > Compiler
> > Intel 2011-0-084 (version 12)
> > Config.h file attached
> >
> >
> > make error:
> > ---------------------------
> > ld: pbsa: hidden symbol `__intel_cpu_indicator_init' in
> >
> /usr/global/intel/composerxe-2011.0.084/compiler/lib/intel64/libirc.a(cpu_disp.o)
> > is referenced by DSO
> > ld: final link failed: Nonrepresentable section on output
> > make[1]: *** [pbsa] Error 1
> > make[1]: Leaving directory
> >
> `/usr/global/amber/intel-2011.0.084-openmpi-1.5/amber11/AmberTools/src/pbsa'
> > make: *** [serial] Error 2
> > --------------------------------------
> >
> >
> >
> > --
> > Dr. Vlad Cojocaru
> > Max Planck Institute for Molecular Biomedicine
> > Department of Cellular and Developmental Biology
> > Roentgenstrasse 20
> > 48149 Muenster, Germany
> > tel: +49-251-70365-324
> > fax: +49-251-70365-399
> > email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 01 2010 - 07:00:04 PST
